SNA Interactive Plotting 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)

SNA Descritive Analysis from “Projeto Redes de Atenção às pessoas que consomem álcool e outras Drogas em Juiz de Fora-MG Brazil” - SNArRDJF

Here you can find a basic script to analysis data from SNArRDJF - this script was elaborated considering its use for orther matrix adjacency data from SNArRDJF - Here we are going to analyse:

1 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)

########################## Basic Preparation ##### `#########################

1.1 Loading objects generated with 1.Principal.Rmd Script - Please run this script only after run 1.Principal.Rmd

1.2 Reload packages

suppressMessages(library(RColorBrewer))
suppressMessages(library(car))
suppressMessages(library(xtable))
suppressMessages(library(igraph))
suppressMessages(library(magrittr))
suppressMessages(library(keyplayer))
suppressMessages(library(dplyr))
suppressMessages(library(visNetwork))
suppressMessages(library(knitr))
suppressMessages(library(DT))

1.3 Adding phantom tools

#In order to get dinamic javascript object install those ones. If you get problems installing go to Stackoverflow.com and type your error to discover what to do. In some cases the libraries need to be intalled in outside R libs.
#devtools::install_github("wch/webshot")
#webshot::install_phantomjs()

1.4 Setting a random seed - this is a good strategy to keep the same graph pattern layout in a new report generation

set.seed(123)

2 Removing CAPS AD

var2_without_CAPS<-delete_vertices(var2,V(var2)[V2_LABEL_ID=="q170_CAPS...CAPS.AD"])

2.1 Vertices and Edges Number

#1. Vertices and Edges
var2_without_CAPS_vcount<-vcount(var2_without_CAPS)
var2_without_CAPS_ecount<-ecount(var2_without_CAPS)

2.2 Vertice Number

Each vertice represents a service - named as an actor in our network

vcount(var2_without_CAPS)

## [1] 186

2.3 Edge Number

Each edge represents a connection between two services named as a tie

ecount(var2_without_CAPS)

## [1] 790

3 Density - The proportion of present edges from all possible edges in the network.

The density of a binary network is simply the proportion of all possible ties that are actually present.

For a valued network, density is defined as the sum of the ties divided by the number of possible ties (i.e. the ratio of all tie strength that is actually present to the number of possible ties).

The density of a network may give us insights into such phenomena as the speed at which information diffuses among the nodes, and the extent to which actors have high levels of social capital and/or social constraint.

3.1 Edge Density

The density of a graph is the ratio of the number of edges and the number of possible edges.

edge_density_var2_without_CAPS<-edge_density(var2_without_CAPS) #The proportion of present edges from all possible edges in the network.
edge_density_var2_without_CAPS

## [1] 0.02295844

3.2 Edge connectivity - Adhesion

The edge connectivity of a graph or two vertices, this is recently also called group adhesion.

edge_connectivity(var2_without_CAPS, source =NULL, target =NULL, checks = T) #source and target can be replaced - their are here just as default

## [1] 0

3.2.1 Adhesion example

In order to use this we need to call source and target using the number of each vertex instead of the name - type in R to get numbers

#Names and numbers

# list all if you have no idea about services id
# V(var2_without_CAPS)$name 

# list all three first (you can use c(1:3))
V(var2_without_CAPS)$name[1]  # just as an example

## [1] "ASS_HOS_ Hospital de Pronto Socorro – HPS"

V(var2_without_CAPS)$name[2]  # just as an example

## [1] "AMB_SAM_ Centro de Atenção à Saúde Mental (CASM)"

V(var2_without_CAPS)$name[3]  # just as an example

## [1] "CRAS_AS_ CRAS Sudeste Costa Carvalho"

# list by others id's
V(var2_without_CAPS)$name[6]  # just as an example

## [1] "ASS_HOS_ Serviço de Controle e Prevenção e Tratamento do Tabagismo (SECOPTT)"

V(var2_without_CAPS)$name[150]  # just as an example

## [1] "UAP_RUR_ Jacutinga"

V(var2_without_CAPS)$name[185]  # just as an example

## [1] "AJU_MUT_ Grupo N.A Rendição"

3.3 Edge Connectivity - “CAPS_AD”==3 and “UAPS RURAL Buiéié”==150

Point connection calculates the number of nodes that would have to be removed in order for one actor to no longer be able to reach another. If there are many different pathways that connect two actors, they have high “connectivity” in the sense that there are multiple ways for a signal to reach from one to the other - lower number - worse resilience

edge_connectivity(var2_without_CAPS, source =150, target =3, checks = T) 

## [1] 0

4 Vertex Connectivity - Group Cohesion

It is the minimum number of vertices needed to remove to make the graph not strongly connected. (If the graph is not strongly connected then this is zero.). The cohesion of a graph (as defined by White and Harary, see references), is the vertex connectivity of the graph. This is calculated by cohesion.

These three functions essentially calculate the same measure(s), more precisely vertex_connectivity is the most general, the other two are included only for the ease of using more descriptive function names.

vertex_connectivity(var2_without_CAPS, source = NULL, target = NULL, checks = TRUE)

## [1] 0

4.1 Cohesion example

In order to use this we need to call source and target using the number of each vertex instead of the name - type in R to get numbers - see example above for more details

4.2 Vertex Connectivity - “CRE_SOC_ CREAS Norte”==6 and “AJU_MUT_ Grupo A.A. Liberdade” ==185

Minimum number of vertices needed to remove to make the vertex not connected by any vertex - it leads an error in case of using two connected vertex

vertex_connectivity(var2_without_CAPS, source =6, target =185, checks = T) 

## [1] 0

5 Centrality Measures

• For undirected graphs:

– Actor centrality - involvement (connections) with other actors

• For directed graphs:

– Actor centrality - source of the ties (outgoing edges)

– Actor prestige - recipient of many ties (incoming edges)

In general - high centrality degree means direct contact with many other actors

5.1 Centrality Degree (number of ties/nearest neighbors).

5.2 Saving in igrpah object

V(var2_without_CAPS)$var2_indegree<-degree(var2_without_CAPS, mode = "in") # Actor prestige - recipient of many ties (incoming edges)
V(var2_without_CAPS)$var2_outdegree <- degree(var2_without_CAPS, mode = "out") # Actor centrality - source of the ties (outgoing edges)
V(var2_without_CAPS)$var2_totaldegree <- degree(var2_without_CAPS, mode = "total")

5.3 Saving in Global Environment as an object

var2_without_CAPS_indegree<-degree(var2_without_CAPS, mode = "in")
var2_without_CAPS_outdegree<-degree(var2_without_CAPS, mode = "out")
var2_without_CAPS_totaldegree<-degree(var2_without_CAPS, mode = "total")

6 Centrality Degree Descriptive Statistics - non-normalized

6.1 Centrality Degree Descriptive Statistics - In

##in
summary(var2_without_CAPS_indegree)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   3.000   4.247   5.000  30.000

sd(var2_without_CAPS_indegree)

## [1] 4.403085

6.2 Histogram var2_without_CAPS degree - In

hist(degree(var2_without_CAPS, mode = "in", normalized = F), ylab="Frequency", xlab="Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Indegree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

6.3 Centrality Degree Descriptive Statistics - Out

##out
summary(var2_without_CAPS_outdegree)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   0.000   1.000   4.247   4.000  88.000

sd(var2_without_CAPS_outdegree)

## [1] 10.16635

6.4 Histogram var2_without_CAPS degree - Out

hist(degree(var2_without_CAPS, mode = "out", normalized = F), ylab="Frequency", xlab="Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Outdegree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

6.5 Centrality Degree Descriptive Statistics - All

##all
summary(var2_without_CAPS_totaldegree)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   4.000   8.495   9.000 118.000

sd(var2_without_CAPS_totaldegree)

## [1] 12.99033

6.6 Histogram var2_without_CAPS degree - All

hist(degree(var2_without_CAPS, mode = "all", normalized = F), ylab="Frequency", xlab="Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of All Degree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

7 Compute strength - weighted

A slightly more nuanced metric is “strength centrality”, which is defined as the sum of the weights of all the connections for a given node. This is also sometimes called “weighted degree centrality”

V(var2_without_CAPS)$var2_strength<- strength(var2_without_CAPS, weights=E(var2_without_CAPS)$weight)
var2_strength<- strength(var2_without_CAPS, weights=E(var2_without_CAPS)$weight)

7.1 Strength Stats

summary(var2_strength)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   4.000   8.495   9.000 118.000

sd(var2_strength)

## [1] 12.99033

7.2 Histogram var2_without_CAPS degree - All

hist(strength(var2_without_CAPS, weights=E(var2_without_CAPS)$weight), ylab="Frequency", xlab="Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Strength Degree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

8 Centrality Degree Normalized

8.1 Centrality Degree Normalized saving igraph object

V(var2_without_CAPS)$var2_indegree_n<-degree(var2_without_CAPS, mode = "in", normalized = T)
V(var2_without_CAPS)$var2_outdegree_n<- degree(var2_without_CAPS, mode = "out", normalized = T)
V(var2_without_CAPS)$var2_totaldegree_n<- degree(var2_without_CAPS, mode = "total", normalized = T)

8.2 Saving in Global Environment as an object

var2_without_CAPS_indegree_n<-degree(var2_without_CAPS, mode = "in", normalized = T)
var2_without_CAPS_outdegree_n<-degree(var2_without_CAPS, mode = "out", normalized = T)
var2_without_CAPS_totaldegree_n<-degree(var2_without_CAPS, mode = "total", normalized = T)

8.3 Centrality Degree Normalized Descriptive Statistics - in

summary(var2_without_CAPS_indegree_n)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## 0.00000 0.01081 0.01622 0.02296 0.02703 0.16220

sd(var2_without_CAPS_indegree_n)

## [1] 0.02380046

8.4 Histogram var2_without_CAPS degree normalized - in

hist(degree(var2_without_CAPS, mode = "in", normalized = T), ylab="Frequency", xlab="Normalized Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Normalized Indegree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

8.5 Centrality Degree Normalized Descriptive Statistics - out

summary(var2_without_CAPS_outdegree_n)

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.000000 0.000000 0.005405 0.022960 0.021620 0.475700

sd(var2_without_CAPS_outdegree_n)

## [1] 0.05495326

8.6 Histogram var2_without_CAPS degree normalized - out

hist(degree(var2_without_CAPS, mode = "out", normalized = T), ylab="Frequency", xlab="Normalized Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Normalized Outdegree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

8.7 Centrality Degree Normalized Descriptive Statistics - all

summary(var2_without_CAPS_totaldegree_n)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## 0.00000 0.01081 0.02162 0.04592 0.04865 0.63780

sd(var2_without_CAPS_totaldegree_n)

## [1] 0.07021799

8.8 Histogram var2_without_CAPS degree normalized - all

hist(degree(var2_without_CAPS, mode = "all", normalized = T), ylab="Frequency", xlab="Normalized Degree",  breaks=vcount(var2_without_CAPS)/10, main="Histogram of Normalized All Degree Nodes - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

9 Centralization Degree

V(var2_without_CAPS)$var2_centr_degree <- centralization.degree(var2_without_CAPS)$res
var2_centr_degree <- centralization.degree(var2_without_CAPS)

9.1 Centralization

var2_centr_degree$centralization

## [1] 0.2975603

9.2 Theoretical Max

var2_centr_degree$theoretical_max

## [1] 68450

10 Degree distribution considering total equal one

var2_without_CAPS_degree.distribution<-degree.distribution(var2_without_CAPS)

10.1 Degree distribution Descriptive Stats

summary(var2_without_CAPS_degree.distribution)

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.000000 0.000000 0.000000 0.008403 0.005376 0.215100

sd(var2_without_CAPS_degree.distribution)

## [1] 0.02712338

10.2 Histogram var2_without_CAPS distribution degree

hist(degree.distribution(var2_without_CAPS), breaks=vcount(var2_without_CAPS)/10, ylab="Frequency", xlab="Degree Distribuition", main="Histogram of Degree Distribuition - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)")

10.3 Degree Probability Distribution

dd <- degree.distribution(var2_without_CAPS, cumulative=T, mode="all")

10.4 Degree Probability Distribution - Plot Cumulative Frequency

plot(dd, pch=19, cex=1, col="orange", xlab="Degree", ylab="Cumulative Frequency", main= "Cumulative Frequency of 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2) ")

11 Log-Log Degree Distribution - Scale Free Network - Does it fit to power law ?

dd.var2_without_CAPS <- degree.distribution(var2_without_CAPS)
d <- 1:max(degree(var2_without_CAPS))-1
ind <- (dd.var2_without_CAPS != 0)

11.1 Plot Log-Log Degree Distribution

plot(d[ind], 
     dd.var2_without_CAPS[ind], 
     log="xy", 
     col="blue",
     xlab=c("Log-Degree"), 
     ylab=c("Log-Intensity"),
     main="Log-Log Degree Distribution For 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)"
     )

12 Average Neighbor Degree versus Vertex Degree (log-log scale for 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2))

The neighborhood of a given order y of a vertex v includes all vertices which are closer to v than the order. Ie. order y=0 is always v itself, order 1 is v plus its immediate neighbors, order 2 is order 1 plus the immediate neighbors of the vertices in order 1, etc.

12.1 Simplify graph first

var2_without_CAPS_simplified<-simplify(var2_without_CAPS)

12.2 Average Neighbor Degree versus vertex degree (log-log scale for var2_without_CAPS)

var2_without_CAPS_a.nn.deg <- graph.knn(var2_without_CAPS_simplified, weights =E(var2_without_CAPS_simplified)$weight)$knn %>% round(1)

12.3 Saving to igraph object

V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg <- graph.knn(var2_without_CAPS_simplified, weights=E(var2_without_CAPS_simplified)$weight)$knn

12.4 Table Average Neighbor Degree

d<-cbind(V(var2_without_CAPS_simplified)$LABEL_COR,var2_without_CAPS_a.nn.deg)
datatable(d)

12.5 Plotting Average Neighbor Degree versus vertex degree

plot(degree(var2_without_CAPS_simplified), 
     var2_without_CAPS_a.nn.deg, 
     log="xy", 
     col="goldenrod", 
     xlab=c("Log Vertex Degree"),
     ylab=c("Log Average Neighbor Degree"),
     main="Average Neighbor Degree vs Vertex Degree - Log-Log Scale for 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)"
     )

13 Average Weighted Neighbor Degree versus vertex degree (log-log scale for weighted 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2))

var2_without_CAPS_a.nn.deg_w <- graph.knn(var2_without_CAPS_simplified, weights=E(var2_without_CAPS_simplified)$weight)$knn %>% round(1)

13.1 Saving to igraph object

V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w <-var2_without_CAPS_a.nn.deg <- graph.knn(var2_without_CAPS_simplified, weights=E(var2_without_CAPS_simplified)$weight)$knn

13.2 Average Weighted Neighbor Descriptive

summary(var2_without_CAPS_a.nn.deg_w)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    2.00   23.50   36.50   39.48   54.00  118.00       7

sd(var2_without_CAPS_a.nn.deg_w, na.rm = T)

## [1] 22.4451

13.3 Table Average Neighbor Degree Weighted

d<-cbind(V(var2_without_CAPS_simplified)$LABEL_COR,var2_without_CAPS_a.nn.deg_w)
datatable(d)

13.4 Plotting Average Neighbor Degree versus vertex degree

plot(degree(var2_without_CAPS_simplified), 
     var2_without_CAPS_a.nn.deg, 
     log="xy", 
     col="goldenrod", 
     xlab=c("Log Vertex Degree"),
     ylab=c("Log Average Neighbor Degree"),
     main="Average Weighted Neighbor Degree vs Vertex Degree - Log-Log Scale For Weighted 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)"
     )

14 Degree Centralities Dinamic Table

14.1 Getting Degree Measures

var2_without_CAPS_indegree<-degree(var2_without_CAPS, mode = "in")
var2_without_CAPS_outdegree<-degree(var2_without_CAPS, mode = "out")
var2_without_CAPS_totaldegree<-degree(var2_without_CAPS, mode = "total")
var2_strength<- strength(var2_without_CAPS, weights=E(var2_without_CAPS)$weight)
var2_without_CAPS_indegree_n<-degree(var2_without_CAPS, mode = "in", normalized = T) %>% round(3)
var2_without_CAPS_outdegree_n<-degree(var2_without_CAPS, mode = "out", normalized = T) %>% round(3)
var2_without_CAPS_totaldegree_n<-degree(var2_without_CAPS, mode = "total", normalized = T) %>% round(3)
var2_centr_degree <- centralization.degree(var2_without_CAPS)$res
var2_without_CAPS_a.nn.deg <- graph.knn(var2_without_CAPS_simplified)$knn %>% round(1)
var2_without_CAPS_a.nn.deg_w <- graph.knn(var2_without_CAPS_simplified, weights=E(var2_without_CAPS_simplified)$weight)$knn %>% round(1)

14.2 Creating a dataframe of measures

var2_without_CAPS_df_degree <- data.frame(var2_without_CAPS_indegree,
var2_without_CAPS_outdegree, 
var2_without_CAPS_totaldegree,
var2_without_CAPS_indegree_n, 
var2_without_CAPS_outdegree_n,
var2_without_CAPS_totaldegree_n,
var2_strength,
var2_centr_degree,
var2_without_CAPS_a.nn.deg,
var2_without_CAPS_a.nn.deg_w) %>% round(3)

#Adding type
var2_without_CAPS_df_degree <-cbind(var2_without_CAPS_df_degree, V(var2_without_CAPS)$LABEL_COR)

#Adding names
names(var2_without_CAPS_df_degree) <- c("In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree","Type")

#Ordering Variables
var2_without_CAPS_df_degree<-var2_without_CAPS_df_degree[c("Type","In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree")]

14.3 General tabel - DT

datatable(var2_without_CAPS_df_degree, filter = 'top')

14.4 Aggregating data from previous table - mean

aggdata_mean <-aggregate(. ~ Type, var2_without_CAPS_df_degree, function(x) c(mean=mean(x)))

#Removing Type variable
names(aggdata_mean) <- c("Group", "In Degree(M)", "Out Degree(M)", "Total Degree(M)","In Degree Normalized(M)", "Out Degree Normalized(M)", "Total Degree Normalized(M)", "Strength(M)","Centralization Degree(M)","Average Neighbor Degree(M)","Average Weighted Neighbor Degree(M)")

14.5 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_degree, function(x) c(median=median(x)))

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]
names(aggdata_median) <- c("Group", "In Degree(median)", "Out Degree(median)", "Total Degree(median)","In Degree Normalized(median)", "Out Degree Normalized(median)", "Total Degree Normalized(median)", "Strength(median)","Centralization Degree(median)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(median)")

14.6 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(2) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Degree(M)","In Degree(median)", "Out Degree(M)", "Out Degree(median)","Total Degree(M)", "Total Degree(median)", "In Degree Normalized(M)", "In Degree Normalized(median)", "Out Degree Normalized(M)", "Out Degree Normalized(median)", "Total Degree Normalized(M)", "Total Degree Normalized(median)", "Strength(M)","Strength(median)", "Centralization Degree(M)","Centralization Degree(median)","Average Neighbor Degree(M)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(M)", "Average Weighted Neighbor Degree(median)")]

14.7 Plotting final table with round

datatable(total_table, filter = 'top')

14.8 Creating a dataframe of measures (Natureza Governamental)

var2_without_CAPS_df_degree <- data.frame(var2_without_CAPS_indegree,
var2_without_CAPS_outdegree, 
var2_without_CAPS_totaldegree,
var2_without_CAPS_indegree_n, 
var2_without_CAPS_outdegree_n,
var2_without_CAPS_totaldegree_n,
var2_strength,
var2_centr_degree,
var2_without_CAPS_a.nn.deg,
var2_without_CAPS_a.nn.deg_w) %>% round(3)

#Adding type
var2_without_CAPS_df_degree <-cbind(var2_without_CAPS_df_degree, V(var2_without_CAPS)$TIPO1)

#Adding names
names(var2_without_CAPS_df_degree) <- c("In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree","Type")

#Ordering Variables
var2_without_CAPS_df_degree<-var2_without_CAPS_df_degree[c("Type","In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree")]

14.9 General tabel - DT

datatable(var2_without_CAPS_df_degree, filter = 'top')

14.10 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_degree, by=list(var2_without_CAPS_df_degree$Type), FUN=mean, na.rm=TRUE)

#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]
names(aggdata_mean) <- c("Group", "In Degree(M)", "Out Degree(M)", "Total Degree(M)","In Degree Normalized(M)", "Out Degree Normalized(M)", "Total Degree Normalized(M)", "Strength(M)","Centralization Degree(M)","Average Neighbor Degree(M)","Average Weighted Neighbor Degree(M)")

14.11 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_degree, function(x) c(median=median(x)))

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]
names(aggdata_median) <- c("Group", "In Degree(median)", "Out Degree(median)", "Total Degree(median)","In Degree Normalized(median)", "Out Degree Normalized(median)", "Total Degree Normalized(median)", "Strength(median)","Centralization Degree(median)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(median)")

14.12 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(2) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Degree(M)","In Degree(median)", "Out Degree(M)", "Out Degree(median)","Total Degree(M)", "Total Degree(median)", "In Degree Normalized(M)", "In Degree Normalized(median)", "Out Degree Normalized(M)", "Out Degree Normalized(median)", "Total Degree Normalized(M)", "Total Degree Normalized(median)", "Strength(M)","Strength(median)", "Centralization Degree(M)","Centralization Degree(median)","Average Neighbor Degree(M)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(M)", "Average Weighted Neighbor Degree(median)")]

14.13 Plotting final table with round

datatable(total_table, filter = 'top')

14.14 Creating a dataframe of measures (Setores)

var2_without_CAPS_df_degree <- data.frame(var2_without_CAPS_indegree,
var2_without_CAPS_outdegree, 
var2_without_CAPS_totaldegree,
var2_without_CAPS_indegree_n, 
var2_without_CAPS_outdegree_n,
var2_without_CAPS_totaldegree_n,
var2_strength,
var2_centr_degree,
var2_without_CAPS_a.nn.deg,
var2_without_CAPS_a.nn.deg_w) %>% round(3)

#Adding type
var2_without_CAPS_df_degree <-cbind(var2_without_CAPS_df_degree, V(var2_without_CAPS)$TIPO2)

#Adding names
names(var2_without_CAPS_df_degree) <- c("In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree","Type")

#Ordering Variables
var2_without_CAPS_df_degree<-var2_without_CAPS_df_degree[c("Type","In Degree", "Out Degree", "Total Degree","In Degree Normalized", "Out Degree Normalized", "Total Degree Normalized", "Strength","Centralization Degree","Average Neighbor Degree","Average Weighted Neighbor Degree")]

14.15 General tabel - DT

datatable(var2_without_CAPS_df_degree, filter = 'top')

14.16 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_degree, by=list(var2_without_CAPS_df_degree$Type), FUN=mean, na.rm=TRUE)

#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]
names(aggdata_mean) <- c("Group", "In Degree(M)", "Out Degree(M)", "Total Degree(M)","In Degree Normalized(M)", "Out Degree Normalized(M)", "Total Degree Normalized(M)", "Strength(M)","Centralization Degree(M)","Average Neighbor Degree(M)","Average Weighted Neighbor Degree(M)")

14.17 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_degree, function(x) c(median=median(x)))

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]
names(aggdata_median) <- c("Group", "In Degree(median)", "Out Degree(median)", "Total Degree(median)","In Degree Normalized(median)", "Out Degree Normalized(median)", "Total Degree Normalized(median)", "Strength(median)","Centralization Degree(median)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(median)")

14.18 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(2) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Degree(M)","In Degree(median)", "Out Degree(M)", "Out Degree(median)","Total Degree(M)", "Total Degree(median)", "In Degree Normalized(M)", "In Degree Normalized(median)", "Out Degree Normalized(M)", "Out Degree Normalized(median)", "Total Degree Normalized(M)", "Total Degree Normalized(median)", "Strength(M)","Strength(median)", "Centralization Degree(M)","Centralization Degree(median)","Average Neighbor Degree(M)","Average Neighbor Degree(median)","Average Weighted Neighbor Degree(M)", "Average Weighted Neighbor Degree(median)")]

14.19 Plotting final table with round

datatable(total_table, filter = 'top')

15 Network plotting based only on degree measures

#Set Seed
set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)

#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$color[edge.start],
     edge.arrow.size=(degree(var2_without_CAPS)+1)/(100*mean(degree(var2_without_CAPS))),
     edge.width=E(var2_without_CAPS)$weight/(10*mean(E(var2_without_CAPS)$weight)),
     edge.curved = TRUE,
     vertex.size=log((degree(var2_without_CAPS)+2))*(0.5*mean(degree(var2_without_CAPS))),
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=log(degree(var2_without_CAPS)+2)/mean(degree(var2_without_CAPS)),
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$LABEL_COR
b<-V(var2_without_CAPS)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .5)

#Adding Title
  title("Network Vertex Degree Sized - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ", cex = .5)
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Median In Degree: %.2f\n Median Out Degree: %.2f",
     median(degree(var2_without_CAPS, mode="in")), 
     median(degree(var2_without_CAPS, mode="out"))
   ))

16 Network plotting based only on degree measures

#Set Seed
set.seed(123)

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-V(var2_without_CAPS)$var2_totaldegree %>% round(1)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<- var2_vertex_color_degree[as.numeric(cut(degree(var2_without_CAPS),breaks =length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)

#PLotting
plot(var2_without_CAPS, 
     layout=co,
     #edge.color=V(var2_without_CAPS)$color[edge.start],
     edge.arrow.size=(degree(var2_without_CAPS)+1)/3000,
     edge.width=E(var2_without_CAPS)$weight/10,
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=log((degree(var2_without_CAPS)+2))*10,
     vertex.size=20,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=log((degree(var2_without_CAPS)+2))/10,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Vertex Degree Sized and Red to Blue - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Median In Degree: %.2f\nMedian Out Degree: %.2f",
     median(degree(var2_without_CAPS, mode="in")), 
     median(degree(var2_without_CAPS, mode="out"))
   ))

17 Network Plotting Centralization - Degree Measures - Using Spectral Color as Distance Measure Representation

#Set Seed
set.seed(123)

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-V(var2_without_CAPS)$var2_centr_degree

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "Spectral"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<- var2_vertex_color_degree[as.numeric(cut(V(var2_without_CAPS)$var2_color_degree,breaks =length(unique(V(var2_without_CAPS)$var2_color_degree))))]

#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)

#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=(degree(var2_without_CAPS)+1)/10000,
     edge.width=E(var2_without_CAPS)$weight/10,
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=log((V(var2_without_CAPS)$var2_centr_degree+2))*10,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=log((degree(var2_without_CAPS)+2))/10,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Vertex Centralization Degree Sized Spectral Colored - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Median In Degree: %.2f\nMedian Out Degree: %.2f",
     median(degree(var2_without_CAPS, mode="in")), 
     median(degree(var2_without_CAPS, mode="out"))
   ))

18 Alternative vizualization using degree in order to genarete sub-graphs - Higher than median degree network

#Set Seed
set.seed(123)

# Network elements with lower than meadian degree
higherthanmedian.network_var2_without_CAPS<-V(var2_without_CAPS)[degree(var2_without_CAPS)<median(degree(var2_without_CAPS))] 

#Deleting vertices based in intersection betewenn var2_without_CAPS 
high_var2_without_CAPS<-delete.vertices(var2_without_CAPS, higherthanmedian.network_var2_without_CAPS)

#Plotting based only on degree measures 
edge.start <- ends(high_var2_without_CAPS, es=E(high_var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(high_var2_without_CAPS))
maxC <- rep(Inf, vcount(high_var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(high_var2_without_CAPS, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(high_var2_without_CAPS)$weight)

#PLotting
plot(high_var2_without_CAPS, 
     layout=co,
     edge.color=V(high_var2_without_CAPS)$color[edge.start],
     edge.arrow.size=(degree(high_var2_without_CAPS)+1)/1000,
     edge.width=E(high_var2_without_CAPS)$weight/10,
     edge.curved = TRUE,
     vertex.size=log((V(high_var2_without_CAPS)$var2_centr_degree+2))*10,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(high_var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=log((degree(high_var2_without_CAPS)+2))/10,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(high_var2_without_CAPS)$LABEL_COR
b<-V(high_var2_without_CAPS)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=3,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .5)

#Adding Title
  title("Network Higher Than Median Degree - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Mean In Degree: %.2f\n Mean Out Degree: %.2f",
     mean(degree(high_var2_without_CAPS, mode="in")), 
     mean(degree(high_var2_without_CAPS, mode="out"))
   )
  )

19 Alternative vizualization using degree in order to genarete sub-graphs - Lower than median degree network

#Set Seed
set.seed(123)

# Network elements with lower than meadian degree
lowerthanmedian.network_var2_without_CAPS<-V(var2_without_CAPS)[degree(var2_without_CAPS)>median(degree(var2_without_CAPS))] 

#Deleting vertices based in intersection betewenn var2_without_CAPS 
small_var2_without_CAPS<-delete.vertices(var2_without_CAPS, lowerthanmedian.network_var2_without_CAPS)

#Plotting based only on degree measures 
edge.start <- ends(small_var2_without_CAPS, es=E(small_var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(small_var2_without_CAPS))
maxC <- rep(Inf, vcount(small_var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(small_var2_without_CAPS, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(small_var2_without_CAPS)$weight)

#PLotting
plot(small_var2_without_CAPS, 
     layout=co,
     edge.color=V(small_var2_without_CAPS)$color[edge.start],
     edge.arrow.size=(degree(small_var2_without_CAPS)+1)/1000,
     edge.width=E(small_var2_without_CAPS)$weight/10,
     edge.curved = TRUE,
     vertex.size=log((V(small_var2_without_CAPS)$var2_centr_degree+2))*20,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(small_var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=log((degree(small_var2_without_CAPS)+2))/3,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)

#Solving Problems with legend rendering 
a<-V(small_var2_without_CAPS)$LABEL_COR
b<-V(small_var2_without_CAPS)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=4,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .5)

#Adding Title
  title("Network Smaller Than Median Degree - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Mean In Degree: %.2f\nMean Out Degree: %.2f",
     mean(degree(small_var2_without_CAPS, mode="in")), 
     mean(degree(small_var2_without_CAPS, mode="out"))
   )
  )

20 Plotting using Average Neighbor Degree

#Set Seed
set.seed(123)

#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS_simplified, es=E(var2_without_CAPS_simplified), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS_simplified))
maxC <- rep(Inf, vcount(var2_without_CAPS_simplified))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS_simplified, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS_simplified)$weight)

#Plotting based only on degree measures  #var2_without_CAPS_simplified_a.nn.deg
V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg<-as.numeric(graph.knn(var2_without_CAPS_simplified)$knn)
V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg[V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg=="NaN"]<-0

#PLotting
plot(var2_without_CAPS_simplified, 
     layout=co,
     edge.color=V(var2_without_CAPS_simplified)$color[edge.start],
     edge.arrow.size=sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg)^2+1)/1000,
     edge.width=E(var2_without_CAPS_simplified)$weight/80,
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS_simplified)$color,
     vertex.size=(sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg)^2))/1,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS_simplified,"LABEL_COR"),
     vertex.label.cex=(sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg)^2)+1)/250,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS_simplified)$LABEL_COR
b<-V(var2_without_CAPS_simplified)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       inset=2,
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=3,
       lwd=2,
       x.intersp=2,
       y.intersp=4,
       cex = .3)

#Adding Title
  title("Network Average Neighbor Degree Sized - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Median Average Neighbor Degree: %.2f",
     median((var2_without_CAPS_a.nn.deg+1))
   ))

21 Plotting using Average Neighbor Degree

#Set Seed
set.seed(123)

#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS_simplified, es=E(var2_without_CAPS_simplified), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS_simplified))
maxC <- rep(Inf, vcount(var2_without_CAPS_simplified))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS_simplified, niter=10000, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS_simplified)$weight)


#Plotting based only on degree measures  #var2_without_CAPS_a.nn.deg
V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w<-as.numeric(graph.knn(var2_without_CAPS_simplified, weights = E(var2_without_CAPS_simplified)$weight)$knn)
V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w[V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w=="NaN"]<-0

#PLotting
plot(var2_without_CAPS_simplified, 
     layout=co,
     edge.color=V(var2_without_CAPS_simplified)$color[edge.start],
     edge.arrow.size=sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w)^2+1)/1000,
     edge.width=E(var2_without_CAPS_simplified)$weight/100,
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS_simplified)$color,
     vertex.size=(sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w)^2))/5,
     vertex.frame.color="#ffffff",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS_simplified,"LABEL_COR"),
     vertex.label.cex=(sqrt((V(var2_without_CAPS_simplified)$var2_without_CAPS_a.nn.deg_w)^2)+1)/500,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2]))
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS_simplified)$LABEL_COR
b<-V(var2_without_CAPS_simplified)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=4,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .5)

#Adding Title
  title("Network Average Weighted Neighbor Degree Sized - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text(x=range(co[,1])[1], y=range(co[,2])[1], labels = 
   sprintf("Median Average Weighted Neighbor Degree: %.2f",
     median((var2_without_CAPS_a.nn.deg_w+1))
   ))

22 Circle Degree Too intensive computation #code

#Circle Degree ***Too intense computation***
#A_var2_without_CAPS <- get.adjacency(var2_without_CAPS, sparse=FALSE)
#detach("package:igraph", unload=TRUE)
#library(network)
#g <- network::as.network.matrix(A_var2_without_CAPS)
#library(sna)
#gplot.target(g, degree(g), main="Circle Degree")
#library(igraph)

23 Closeness - centrality based on distance to others in the graph

How close an actor to all the other actors in network?

High closeness centrality - short communication path to others, minimal number of steps to reach others.

Answers the “Kevin Bacon” question:

How many steps are required to access every other vertex from a given vertex?

One practical implication of this metric: it helps you gauge how information might spread within your network, and who might be the best people to leverage if you need to make sure information gets around. Link here: http://www.tc.umn.edu/~alink/R-social-network-analysis.html

Closeness centrality can be defined as a measure of how far other nodes are from the node in question. Nodes with high closeness centrality are likely to be relatively efficient in receiving or transmitting information to/from distant parts of the social network.

Scores may be interpreted as arising from a reciprocal process in which the centrality of each actor is proportional to the sum of the centralities of those actors to whom he or she is connected.

In general, vertices with high eigenvector centralities are those which are connected to many other vertices which are, in turn, connected to many others (and so on). (The perceptive may realize that this implies that the largest values will be obtained by individuals in large cliques (or high-density substructures)

23.1 Closeness Non-normalized

23.1.1 Saving to Igraph object

V(var2_without_CAPS)$var2_incloseness <- closeness(var2_without_CAPS, mode = "in", weights = E(var2_without_CAPS)$var2) %>% round(6)
V(var2_without_CAPS)$var2_outcloseness <- closeness(var2_without_CAPS, mode = "out", weights = E(var2_without_CAPS)$var2) %>% round(6)
V(var2_without_CAPS)$var2_totalcloseness <- closeness(var2_without_CAPS, mode = "total", weights = E(var2_without_CAPS)$var2) %>% round(4)

23.1.2 Saving to Environment

var2_without_CAPS_incloseness<- closeness(var2_without_CAPS, mode = "in", weights = E(var2_without_CAPS)$var2) %>% round(6)
var2_without_CAPS_outcloseness<- closeness(var2_without_CAPS, mode = "out", weights = E(var2_without_CAPS)$var2) %>% round(6)
var2_without_CAPS_totalcloseness<- closeness(var2_without_CAPS, mode = "total", weights = E(var2_without_CAPS)$var2) %>% round(6)

23.2 Closeness Non-normalized - IN

summary(var2_without_CAPS_incloseness)

##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## 2.900e-05 5.500e-05 5.500e-05 5.426e-05 5.600e-05 5.900e-05

sd(var2_without_CAPS_incloseness)

## [1] 5.422721e-06

23.2.1 Network Plotting Based On Non-normalized Closeness - IN

V(var2_without_CAPS)$var2_incloseness<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in")

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_incloseness,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in"),
     edge.width=E(var2_without_CAPS)$weight/mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in")*10^5,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=(closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in")+10^-5)*2000,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized and Colored In - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median In Closennes:%.4f\nSD In Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="in", weights = E(var2_without_CAPS)$var2)), 
             sd(closeness(var2_without_CAPS, mode="in", weights = E(var2_without_CAPS)$var2))
             )
       )

23.3 Closeness Non-normalized - OUT

summary(var2_without_CAPS_outcloseness)

##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## 0.0000290 0.0000290 0.0000300 0.0002438 0.0004738 0.0005190

sd(var2_without_CAPS_outcloseness)

## [1] 0.0002231169

23.3.1 Network Plotting Based On Non-normalized Closeness - OUT

V(var2_without_CAPS)$var2_outcloseness<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out")

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_outcloseness,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out"),
     edge.width=E(var2_without_CAPS)$weight/2*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out")*10^4,
     vertex.frame.color="white",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out")*200,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized and Colored OUT - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median OUT Closennes:%.4f\nSD OUT Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="out", weights = E(var2_without_CAPS)$var2)), 
             sd(closeness(var2_without_CAPS, mode="out", weights = E(var2_without_CAPS)$var2))
             )
       )

23.4 Closeness Non-normalized - ALL

summary(var2_without_CAPS_totalcloseness)

##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## 0.0000290 0.0005290 0.0005690 0.0005403 0.0005738 0.0006270

sd(var2_without_CAPS_totalcloseness)

## [1] 0.0001041298

23.4.1 Network Plotting Based On Non-normalized Closeness - ALL

V(var2_without_CAPS)$var2_allcloseness<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all")

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_allcloseness,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all"),
     edge.width=E(var2_without_CAPS)$weight/2*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all")*10^4,
     vertex.frame.color="white",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=(closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all")+0.00001)*200,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized and Colored all - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median all Closennes:%.4f\nSD all Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="all", weights = E(var2_without_CAPS)$var2)), 
             sd(closeness(var2_without_CAPS, mode="all", weights = E(var2_without_CAPS)$var2))
             )
       )

23.5 Closeness Normalized

23.5.1 Saving to Igraph object

V(var2_without_CAPS)$var2_incloseness_n <- closeness(var2_without_CAPS, mode = "in",, weights = E(var2_without_CAPS)$var2, normalized = T) %>% round(10)
V(var2_without_CAPS)$var2_outcloseness_n <- closeness(var2_without_CAPS, mode = "out", normalized = T, weights = E(var2_without_CAPS)$var2) %>% round(6)
V(var2_without_CAPS)$var2_totalcloseness_n <- closeness(var2_without_CAPS, mode = "total", normalized = T, weights = E(var2_without_CAPS)$var2) %>% round(6)

23.5.2 Saving to Environment

var2_without_CAPS_incloseness_n<- closeness(var2_without_CAPS, mode = "in", normalized = T, weights = E(var2_without_CAPS)$var2) %>% round(6)
var2_without_CAPS_outcloseness_n<- closeness(var2_without_CAPS, mode = "out", normalized = T, weights = E(var2_without_CAPS)$var2) %>% round(6)
var2_without_CAPS_totalcloseness_n<- closeness(var2_without_CAPS, mode = "total", normalized = T, weights = E(var2_without_CAPS)$var2) %>% round(6)

23.5.3 Closeness Normalized - IN

summary(var2_without_CAPS_incloseness_n)

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.005376 0.010170 0.010230 0.010040 0.010330 0.010850

sd(var2_without_CAPS_incloseness_n)

## [1] 0.0009996134

23.6 Network Plotting Based On Normalized Closeness - IN

V(var2_without_CAPS)$var2_incloseness_n<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in", normalized = T)

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_incloseness_n,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in",normalized = T),
     edge.width=E(var2_without_CAPS)$weight/1000*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=(closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in",normalized = T))*10000,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="in",normalized = T)*10,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized Normalized In - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median In Closennes:%.4f\nSD In Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="in", weights = E(var2_without_CAPS)$var2, normalized = T)), 
             sd(closeness(var2_without_CAPS, mode="in", weights = E(var2_without_CAPS)$var2, normalized = T))
             )
       )

###Closeness Normalized - OUT

summary(var2_without_CAPS_outcloseness_n)

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.005376 0.005376 0.005555 0.045110 0.087640 0.096050

sd(var2_without_CAPS_outcloseness_n)

## [1] 0.04126991

23.7 Network Plotting Based On Normalized Closeness - OUT

V(var2_without_CAPS)$var2_outcloseness_n<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out", normalized = T)

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_outcloseness_n,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out",normalized = T),
     edge.width=E(var2_without_CAPS)$weight/10*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=(closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out",normalized = T))*100,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out",normalized = T)*1.5,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized Normalized OUT - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median OUT Closennes:%.4f\nSD OUT Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="out", weights = E(var2_without_CAPS)$var2, normalized = T)), 
             sd(closeness(var2_without_CAPS, mode="out", weights = E(var2_without_CAPS)$var2, normalized = T))
             )
       )

23.7.1 Closeness Normalized - ALL

summary(var2_without_CAPS_totalcloseness_n)

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.005376 0.097880 0.105200 0.099950 0.106100 0.116000

sd(var2_without_CAPS_totalcloseness_n)

## [1] 0.01926236

23.8 Network Plotting Based On Normalized Closeness - ALL

V(var2_without_CAPS)$var2_allcloseness_n<-closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all", normalized = T)

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_allcloseness_n,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "RdBu"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all",normalized = T),
     edge.width=E(var2_without_CAPS)$weight/10*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=(closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all",normalized = T))*100,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="all",normalized = T)*1.5,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Closeness Degree Sized Normalized ALL - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median ALL Closennes:%.4f\nSD ALL Closennes: %.5f",
             median(closeness(var2_without_CAPS, mode="all", weights = E(var2_without_CAPS)$var2, normalized = T)), 
             sd(closeness(var2_without_CAPS, mode="all", weights = E(var2_without_CAPS)$var2, normalized = T))
             )
       )

23.9 Closeness Normalized

23.9.1 Saving to Igraph object

V(var2_without_CAPS)$var2_incloseness_n <- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "in", normalized = T) %>% round(6)
V(var2_without_CAPS)$var2_outcloseness_n <- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "out", normalized = T) %>% round(6)
V(var2_without_CAPS)$var2_totalcloseness_n <- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "total", normalized = T) %>% round(6)

23.10 Centralization Closseness

V(var2_without_CAPS)$var2_centr_closeness<- centralization.closeness(var2_without_CAPS)$res
var2_centr_closeness<- centralization.closeness(var2_without_CAPS)$res
var2_without_CAPS_centr_closeness_all<- centralization.closeness(var2_without_CAPS)

23.10.1 Centralization

var2_without_CAPS_centr_closeness_all$centralization

## [1] 0.05149328

23.10.2 Theoretical Max

var2_without_CAPS_centr_closeness_all$theoretical_max

## [1] 184.0054

23.11 Network Plotting Based On Centralization Closeness

V(var2_without_CAPS)$var2_centr_closeness<- centralization.closeness(var2_without_CAPS)$res

#Get Variable
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_centr_closeness,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "Spectral"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=centralization.closeness(var2_without_CAPS)$res,
     edge.width=E(var2_without_CAPS)$weight/10*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=centralization.closeness(var2_without_CAPS)$res*100,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=centralization.closeness(var2_without_CAPS)$res,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)


#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
  title("Network Centralization Closeness - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf(
             "Median Centralization Closeness:%.4f\nSD Centralization Closeness: %.5f",
             median(centralization.closeness(var2_without_CAPS)$res), 
             sd(centralization.closeness(var2_without_CAPS)$res)
             )
       )

24 Closeness Dinamic Table

24.1 Getting Closeness Measures

var2_without_CAPS_incloseness<- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "in") %>% round(6)
var2_without_CAPS_outcloseness<- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "out") %>% round(6)
var2_without_CAPS_totalcloseness<- closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode = "total") %>% round(6)
var2_without_CAPS_incloseness_n<- closeness(var2_without_CAPS,weights = E(var2_without_CAPS)$var2, mode = "in", normalized = T) %>% round(6)
var2_without_CAPS_outcloseness_n<- closeness(var2_without_CAPS,weights = E(var2_without_CAPS)$var2, mode = "out", normalized = T) %>% round(6)
var2_without_CAPS_totalcloseness_n<- closeness(var2_without_CAPS,weights = E(var2_without_CAPS)$var2, mode = "total", normalized = T) %>% round(6)
var2_centr_closeness <- centralization.closeness(var2_without_CAPS)$res %>% round(6)

24.2 Creating a datagrame of measures

var2_without_CAPS_df_closseness <- data.frame(
var2_without_CAPS_incloseness,
var2_without_CAPS_outcloseness,
var2_without_CAPS_totalcloseness,
var2_without_CAPS_incloseness_n,
var2_without_CAPS_outcloseness_n,
var2_without_CAPS_totalcloseness_n,
var2_centr_closeness) %>% round(6)

#Adding type
var2_without_CAPS_df_closseness <-cbind(var2_without_CAPS_df_closseness, V(var2_without_CAPS)$LABEL_COR)

#Adding names
names(var2_without_CAPS_df_closseness) <- c("In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized", "Total Closeness Normalized","Centralization Closeness","Type")

#Ordering Variables
var2_without_CAPS_df_closseness<-var2_without_CAPS_df_closseness[c("Type","In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized","Total Closeness Normalized", "Centralization Closeness")]

24.3 General tabel - DT

datatable(var2_without_CAPS_df_closseness, filter = 'top')

24.4 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_closseness, by=list(var2_without_CAPS_df_closseness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","In Closeness(M)", "Out Closeness(M)", "Total Closeness(M)","In Closeness Normalized(M)", "Out Closeness Normalized(M)", "Total Closeness Normalized(M)","Centralization Closeness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

24.5 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_closseness, function(x) c(median=median(x))) 


names(aggdata_median) <- c("Group","In Closeness(median)", "Out Closeness(median)", "Total Closeness(median)","In Closeness Normalized(median)", "Out Closeness Normalized(median)", "Total Closeness Normalized(median)", "Centralization Closeness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

#Merging mean and median
total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(6) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Closeness(M)", "In Closeness(median)", "Out Closeness(M)", "Out Closeness(median)", "Total Closeness(M)","Total Closeness(median)","In Closeness Normalized(M)", "In Closeness Normalized(median)", "Out Closeness Normalized(M)", "Out Closeness Normalized(median)", "Total Closeness Normalized(M)","Total Closeness Normalized(median)", "Centralization Closeness(M)","Centralization Closeness(median)")]

24.6 Plotting final table with round for Closseness

datatable(total_table, filter = 'top')

24.7 Creating a datagrame of measures (Natureza Governamental)

var2_without_CAPS_df_closseness <- data.frame(
var2_without_CAPS_incloseness,
var2_without_CAPS_outcloseness,
var2_without_CAPS_totalcloseness,
var2_without_CAPS_incloseness_n,
var2_without_CAPS_outcloseness_n,
var2_without_CAPS_totalcloseness_n,
var2_centr_closeness) %>% round(6)

#Adding type
var2_without_CAPS_df_closseness <-cbind(var2_without_CAPS_df_closseness, V(var2_without_CAPS)$TIPO1)

#Adding names
names(var2_without_CAPS_df_closseness) <- c("In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized", "Total Closeness Normalized","Centralization Closeness","Type")

#Ordering Variables
var2_without_CAPS_df_closseness<-var2_without_CAPS_df_closseness[c("Type","In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized","Total Closeness Normalized", "Centralization Closeness")]

24.8 General tabel - DT

datatable(var2_without_CAPS_df_closseness, filter = 'top')

24.9 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_closseness, by=list(var2_without_CAPS_df_closseness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","In Closeness(M)", "Out Closeness(M)", "Total Closeness(M)","In Closeness Normalized(M)", "Out Closeness Normalized(M)", "Total Closeness Normalized(M)","Centralization Closeness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

24.10 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_closseness, function(x) c(median=median(x))) 

names(aggdata_median) <- c("Group","In Closeness(median)", "Out Closeness(median)", "Total Closeness(median)","In Closeness Normalized(median)", "Out Closeness Normalized(median)", "Total Closeness Normalized(median)", "Centralization Closeness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

#Merging mean and median
total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(6) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Closeness(M)", "In Closeness(median)", "Out Closeness(M)", "Out Closeness(median)", "Total Closeness(M)","Total Closeness(median)","In Closeness Normalized(M)", "In Closeness Normalized(median)", "Out Closeness Normalized(M)", "Out Closeness Normalized(median)", "Total Closeness Normalized(M)","Total Closeness Normalized(median)", "Centralization Closeness(M)","Centralization Closeness(median)")]

24.11 Plotting final table with round for Closseness

datatable(total_table, filter = 'top')

24.12 Creating a datagrame of measures (Setores)

var2_without_CAPS_df_closseness <- data.frame(
var2_without_CAPS_incloseness,
var2_without_CAPS_outcloseness,
var2_without_CAPS_totalcloseness,
var2_without_CAPS_incloseness_n,
var2_without_CAPS_outcloseness_n,
var2_without_CAPS_totalcloseness_n,
var2_centr_closeness) %>% round(6)

#Adding type
var2_without_CAPS_df_closseness <-cbind(var2_without_CAPS_df_closseness, V(var2_without_CAPS)$TIPO2)

#Adding names
names(var2_without_CAPS_df_closseness) <- c("In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized", "Total Closeness Normalized","Centralization Closeness","Type")

#Ordering Variables
var2_without_CAPS_df_closseness<-var2_without_CAPS_df_closseness[c("Type","In Closeness", "Out Closeness", "Total Closeness","In Closeness Normalized", "Out Closeness Normalized","Total Closeness Normalized", "Centralization Closeness")]

24.13 General tabel - DT

datatable(var2_without_CAPS_df_closseness, filter = 'top')

24.14 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_closseness, by=list(var2_without_CAPS_df_closseness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","In Closeness(M)", "Out Closeness(M)", "Total Closeness(M)","In Closeness Normalized(M)", "Out Closeness Normalized(M)", "Total Closeness Normalized(M)","Centralization Closeness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

24.15 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_closseness, function(x) c(median=median(x))) 

names(aggdata_median) <- c("Group","In Closeness(median)", "Out Closeness(median)", "Total Closeness(median)","In Closeness Normalized(median)", "Out Closeness Normalized(median)", "Total Closeness Normalized(median)", "Centralization Closeness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

#Merging mean and median
total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(6) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","In Closeness(M)", "In Closeness(median)", "Out Closeness(M)", "Out Closeness(median)", "Total Closeness(M)","Total Closeness(median)","In Closeness Normalized(M)", "In Closeness Normalized(median)", "Out Closeness Normalized(M)", "Out Closeness Normalized(median)", "Total Closeness Normalized(M)","Total Closeness Normalized(median)", "Centralization Closeness(M)","Centralization Closeness(median)")]

24.16 Plotting final table with round for Closseness

datatable(total_table, filter = 'top')

25 Betweenness - Number of shortest paths going through the actor σst(i)

High betweenness centrality - vertex lies on many shortest paths. Probability that a communication from s to t will go through i - considering σst(i).

Betweenness measures the number of shortest paths between nodes in the network that go through the node in question. Nodes with relatively high betweenness are likely to be key conduits of information flow across a network, and their removal may have a large impact on spreading phenomena.

25.1 Betweenness Centrality -(Vertex)

Betweenness centrality based on a broker position connecting others or Number of geodesics that pass through the node or the edge. A higher number means an more important node.

26 Adding weight equal one for all analysis

E(var2_without_CAPS)$equalone<-1

26.0.1 Saving objects

V(var2_without_CAPS)$var2_betweenness <- betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$equalone) %>% round(6)
var2_without_CAPS_betweenness <- betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$equalone) %>% round(6)

#Z Score 
V(var2_without_CAPS)$var2_without_CAPS_betweenness_zscore <- (V(var2_without_CAPS)$var2_betweenness - mean(V(var2_without_CAPS)$var2_betweenness))/sd(V(var2_without_CAPS)$var2_betweenness)

#Normalized
V(var2_without_CAPS)$var2_without_CAPS_betweenness_norm <- (V(var2_without_CAPS)$var2_betweenness - min(V(var2_without_CAPS)$var2_betweenness))/max(V(var2_without_CAPS)$var2_betweenness)-min(V(var2_without_CAPS)$var2_betweenness)

26.0.2 Betweenness Centrality - all

summary(var2_without_CAPS_betweenness)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00    0.00    0.00  221.70   58.13 5983.00

sd(var2_without_CAPS_betweenness)

## [1] 711.0878

26.1 Betweenness Centrality Weighted - (Vertex)

V(var2_without_CAPS)$var2_betweenness_w <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$var2) %>% round(6)
var2_betweenness_w <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$var2) %>% round(6)

26.1.1 Descriptive Betweenness Centrality Weighted - (Vertex) - all

summary(var2_betweenness_w)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00    0.00    0.00  221.70   58.13 5983.00

sd(var2_betweenness_w)

## [1] 711.0878

26.2 Centralization Betweenness

V(var2_without_CAPS)$var2_centr_betweenness <- centralization.betweenness(var2_without_CAPS)$res
var2_centr_betweenness <- centralization.betweenness(var2_without_CAPS)

26.2.1 Centralization

var2_centr_betweenness$centralization

## [1] 0.1701532

26.2.2 Theoretical Max

var2_centr_betweenness$theoretical_max

## [1] 6297400

27 Betweenness Vertex Centrality Dinamic Table

#Betweenness Vertex Centrality Measures Dinamic Table
#Getting  Measures
var2_without_CAPS_betweenness <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$equalone) %>% round(6)
var2_betweenness_w <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$var2) %>% round(6)
var2_centr_betweenness <- centralization.betweenness(var2_without_CAPS)$res %>% round(6)

#Creating a dataframe of measures
var2_without_CAPS_df_betweenness <- data.frame(var2_without_CAPS_betweenness,
var2_betweenness_w,
var2_centr_betweenness) %>% round(6)

#Adding type
var2_without_CAPS_df_betweenness <-cbind(var2_without_CAPS_df_betweenness, V(var2_without_CAPS)$LABEL_COR)

#Adding names
names(var2_without_CAPS_df_betweenness) <- c("Betweenness", "Betweenness Weighted", "Centralization Betweenness","Type")

#Ordering Variables
var2_without_CAPS_df_betweenness<-var2_without_CAPS_df_betweenness[c("Type","Betweenness", "Betweenness Weighted", "Centralization Betweenness")]

27.1 General tabel for Betweenness

datatable(var2_without_CAPS_df_betweenness, filter = 'top')

##Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_betweenness, by=list(var2_without_CAPS_df_betweenness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Betweenness(M)", "Betweenness Weighted(M)", "Centralization Betweenness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

27.2 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_betweenness, function(x) c(median=median(x)))  

names(aggdata_median) <- c("Group","Betweenness(median)", "Betweenness Weighted(median)", "Centralization Betweenness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

27.3 Merging mean and median

total_table<- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(1) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Betweenness(M)","Betweenness(median)","Betweenness Weighted(M)", "Betweenness Weighted(median)", "Centralization Betweenness(M)","Centralization Betweenness(median)")]

27.4 Plotting final table with round

datatable(total_table, filter = 'top')

28 Betweenness Vertex Centrality Dinamic Table (Natureza Governamental)

#Betweenness Vertex Centrality Measures Dinamic Table
#Getting  Measures
var2_without_CAPS_betweenness <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$equalone) %>% round(6)
var2_betweenness_w <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$var2) %>% round(6)
var2_centr_betweenness <- centralization.betweenness(var2_without_CAPS)$res %>% round(6)

#Creating a dataframe of measures
var2_without_CAPS_df_betweenness <- data.frame(var2_without_CAPS_betweenness,
var2_betweenness_w,
var2_centr_betweenness) %>% round(6)

#Adding type
var2_without_CAPS_df_betweenness <-cbind(var2_without_CAPS_df_betweenness, V(var2_without_CAPS)$TIPO1)

#Adding names
names(var2_without_CAPS_df_betweenness) <- c("Betweenness", "Betweenness Weighted", "Centralization Betweenness","Type")

#Ordering Variables
var2_without_CAPS_df_betweenness<-var2_without_CAPS_df_betweenness[c("Type","Betweenness", "Betweenness Weighted", "Centralization Betweenness")]

28.1 General tabel for Betweenness

datatable(var2_without_CAPS_df_betweenness, filter = 'top')

##Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_betweenness, by=list(var2_without_CAPS_df_betweenness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Betweenness(M)", "Betweenness Weighted(M)", "Centralization Betweenness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

28.2 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_betweenness, function(x) c(median=median(x)))  

names(aggdata_median) <- c("Group","Betweenness(median)", "Betweenness Weighted(median)", "Centralization Betweenness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

28.3 Merging mean and median

total_table<- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(6) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Betweenness(M)","Betweenness(median)","Betweenness Weighted(M)", "Betweenness Weighted(median)", "Centralization Betweenness(M)","Centralization Betweenness(median)")]

28.4 Plotting final table with round

datatable(total_table, filter = 'top')

29 Betweenness Vertex Centrality Dinamic Table (Setores)

#Betweenness Vertex Centrality Measures Dinamic Table
#Getting  Measures
var2_without_CAPS_betweenness <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$equalone) %>% round(6)
var2_betweenness_w <- betweenness(var2_without_CAPS, weights=E(var2_without_CAPS)$var2) %>% round(1)
var2_centr_betweenness <- centralization.betweenness(var2_without_CAPS)$res %>% round(6)

#Creating a dataframe of measures
var2_without_CAPS_df_betweenness <- data.frame(var2_without_CAPS_betweenness,
var2_betweenness_w,
var2_centr_betweenness) %>% round(6)

#Adding type
var2_without_CAPS_df_betweenness <-cbind(var2_without_CAPS_df_betweenness, V(var2_without_CAPS)$TIPO2)

#Adding names
names(var2_without_CAPS_df_betweenness) <- c("Betweenness", "Betweenness Weighted", "Centralization Betweenness","Type")

#Ordering Variables
var2_without_CAPS_df_betweenness<-var2_without_CAPS_df_betweenness[c("Type","Betweenness", "Betweenness Weighted", "Centralization Betweenness")]

29.1 General tabel for Betweenness

datatable(var2_without_CAPS_df_betweenness, filter = 'top')

29.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_df_betweenness, by=list(var2_without_CAPS_df_betweenness$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Betweenness(M)", "Betweenness Weighted(M)", "Centralization Betweenness(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

29.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_df_betweenness, function(x) c(median=median(x)))  

names(aggdata_median) <- c("Group","Betweenness(median)", "Betweenness Weighted(median)", "Centralization Betweenness(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

29.4 Merging mean and median

total_table<- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(6) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Betweenness(M)","Betweenness(median)","Betweenness Weighted(M)", "Betweenness Weighted(median)", "Centralization Betweenness(M)","Centralization Betweenness(median)")]

29.5 Plotting final table with round

datatable(total_table, filter = 'top')

29.6 Plotting Betweenness Centrality - (Vertex)

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)

#Plotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$color[edge.start],
     edge.arrow.size=(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2)+1)/100000,
     edge.width=E(var2_without_CAPS)$weight/10*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$color,
     vertex.size=betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2 )/150,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2)+1)/10000,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)

#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$LABEL_COR
b<-V(var2_without_CAPS)$color
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

#Adding Title
    title("Network Vertex Betweenness Sized - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels =    sprintf("Median Betweenness: %.2f\nSD Betweenness: %.2f",
     median(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2)), 
     sd(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2))
             )
       )

29.7 Network Plotting Based On Centralization Betweenness

#Get Variable
V(var2_without_CAPS)$var2_centr_betweenness<-(centralization.betweenness(var2_without_CAPS)$res)/100
V(var2_without_CAPS)$var2_color_degree<-round(V(var2_without_CAPS)$var2_centr_betweenness,6)

#Creating brewer pallette
var2_vertex_color_degree<-
  colorRampPalette(brewer.pal(length(unique(
          V(var2_without_CAPS)$var2_color_degree)), "Spectral"))(
            length(unique(V(var2_without_CAPS)$var2_color_degree)))

#Saving as Vertex properties 
V(var2_without_CAPS)$var2_vertex_color_degree<-
  var2_vertex_color_degree[as.numeric(
  cut(V(var2_without_CAPS)$var2_color_degree,
      breaks=length(unique(V(var2_without_CAPS)$var2_color_degree))))]

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS, es=E(var2_without_CAPS), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS))
maxC <- rep(Inf, vcount(var2_without_CAPS))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights = E(var2_without_CAPS)$weight)


#PLotting
plot(var2_without_CAPS, 
     layout=co,
     edge.color=V(var2_without_CAPS)$var2_vertex_color_degree[edge.start],
     edge.arrow.size=closeness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2, mode="out"),
     edge.width=E(var2_without_CAPS)$weight/10*mean(E(var2_without_CAPS)$weight),
     edge.curved = TRUE,
     vertex.color=V(var2_without_CAPS)$var2_vertex_color_degree,
     vertex.size=(centralization.betweenness(var2_without_CAPS)$res+1)/100,
     vertex.frame.color="white",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS,"LABEL_COR"),
     vertex.label.cex=(centralization.betweenness(var2_without_CAPS)$res + 1)/10000,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)

#Solving Problems with legend rendering 
a<-V(var2_without_CAPS)$var2_color_degree
b<-V(var2_without_CAPS)$var2_vertex_color_degree
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
e<-e[order(e$a,decreasing=T),] 
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)

  #Adding Title
  title("Network Centralization Betweenness - 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", sub = "Source: from authors ")
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels = sprintf("Median Betweenness:%.0f\nSDBetweenness: %.0f",
     median(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2)), 
     sd(betweenness(var2_without_CAPS, weights = E(var2_without_CAPS)$var2))
             )
       )

30 Reciprocity Default

Reciprocity Default - Proportion of mutual connections - probability that hte opposite counterpart of a directed graph is also included

reciprocity(var2_without_CAPS, mode="default")

## [1] 0.2556962

31 Reciprocity Ratio

Reciprocity Ratio - Probability of mutual connections between a vertex pair - if we know - probability that hte opposite counterpart of a directed graph is also included in the

reciprocity(var2_without_CAPS, mode="ratio")

## [1] 0.1465893

32 Dyad Census

A dyad consists of an unordered pair of actors and links that exist between two actors of the pair classified by mutal non-mutual and no connection in a directed graphs

Dyads are 2-subgraphs where a subgraph is a subset of actors taken from the complete set of network actors and all links between them. See more here http://file.scirp.org/pdf/SN_2013012915270187.pdf

32.1 Dyad Census

Number of pairs with mutual connections “mut” and number of pairs with non-mutual connections “asym”

dyad.census_var2_without_CAPS<-dyad.census(var2_without_CAPS)

32.2 Mutual connections.

dyad.census_var2_without_CAPS_mut<-dyad.census_var2_without_CAPS$mut
dyad.census_var2_without_CAPS_mut

## [1] 101

32.3 Non-mutual connections.

dyad.census_var2_without_CAPS_asym<-dyad.census_var2_without_CAPS$asym
dyad.census_var2_without_CAPS_asym

## [1] 588

32.4 No connection between them.

dyad.census_var2_without_CAPS_null<-dyad.census_var2_without_CAPS$null
dyad.census_var2_without_CAPS_null

## [1] 16516

33 Triad Census - Check this out in order to understand triad lables

The studies about transitivity in social networks led Holland and Leinhardt (1975) to propose that the local structure in social networks can be expressed by the triad census or triad count, the numbers of triads of any kinds.

You can see more here: http://www.stats.ox.ac.uk/~snijders/Trans_Triads_ha.pdf

#Triad Census 
tc_var2_without_CAPS <- triad.census(var2_without_CAPS)

#Triad Census Label 
census_labels = c('T.003',
                  'T.012',
                  'T.102',
                  'T.021D',
                  'T.021U',
                  'T.021C',
                  'T.111D',
                  'T.111U',
                  'T.030T',
                  'T.030C',
                  'T.201',
                  'T.120D',
                  'T.120U',
                  'T.120C',
                  'T.210',
                  'T.300')

ordering = c('1',
                  '2',
                  '3',
                  '4',
                  '5',
                  '6',
                  '7',
                  '8',
                  '13',
                  '10',
                  '9',
                  '14',
                  '15',
                  '11',
                  '12',
                  '16')

#Saving in a dataframe for further studies
triad_df_var2_without_CAPS <- data.frame(census_labels,tc_var2_without_CAPS)
write.csv(triad_df_var2_without_CAPS, "~/SNArRDJF/Banco Redes R/var2_without_CAPS_complet_triads.csv")

33.1 Triad Census Types

The following labels gives the 16 different triads for directed graphs. The coding refers to the numbers of mutual, asymmetric, and null dyads, with a further identifying letter: Up, Down, Cyclical, Transitive.

E.g., 1-2-0-D has 1 mutual, 2 asymmetric, 0 null dyads, and the Down orientation.

33.1.1 Describing triads

triad_df_var2_without_CAPS

##    census_labels tc_var2_without_CAPS
## 1          T.003               943700
## 2          T.012                82676
## 3          T.102                14558
## 4         T.021D                 6977
## 5         T.021U                 1129
## 6         T.021C                 2187
## 7         T.111D                  560
## 8         T.111U                 2284
## 9         T.030T                  374
## 10        T.030C                   15
## 11         T.201                  239
## 12        T.120D                   70
## 13        T.120U                  265
## 14        T.120C                   73
## 15         T.210                  103
## 16         T.300                   30

33.1.2 Triads Tables Recoding

#Recoding different types of triads 
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.003"]<-"Vacuously Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.012"]<-"Vacuously Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.102"]<-"Vacuously Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.021D"]<-"Vacuously Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.021U"]<-"Vacuously Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.021C"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.111D"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.111U"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.030T"]<-"Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.030C"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.201"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.120D"]<-"Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.120U"]<-"Transitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.120C"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.210"]<-"Intransitive"
triad_df_var2_without_CAPS$type[triad_df_var2_without_CAPS$census_labels=="T.300"]<-"Transitive"

Graphical Ilustration

http://knoesis.wright.edu/sites/default/files/icnc15.pdf

33.1.3 Triads Tables

datatable(triad_df_var2_without_CAPS)

34 Transitivity - clustering coefficient

34.1 Transitivity Global

Socialnetwork is treated as an undirected network global - ratio of triangles (direction disregarded) to connected triples.

transitivity(var2_without_CAPS, type="global")

## [1] 0.1725844

35 Transitivity Local

Ratio of triangles to connected triples each vertex is part of.

V(var2_without_CAPS)$var2_transitivity_local<-transitivity(var2_without_CAPS, type="local") 
var2_without_CAPS_transitivity_local<-transitivity(var2_without_CAPS, type="local") #local - ratio of triangles to connected triples each vertex is part of.

36 Descriptive Statistics for Local Transitivity by Vertex

summary(var2_without_CAPS_transitivity_local[which(var2_without_CAPS_transitivity_local != Inf)])

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.2143  0.3333  0.4724  0.8333  1.0000

sd(var2_without_CAPS_transitivity_local[which(var2_without_CAPS_transitivity_local != Inf)])

## [1] 0.3367331

37 Barrat’s Weighted Transitivity by Edges (Barrat’s)

V(var2_without_CAPS)$var2_transitivity_barrat<-transitivity(var2_without_CAPS, weights=E(var2_without_CAPS)$weight, type="barrat")

var2_without_CAPS_transitivity_barrat<-transitivity(var2_without_CAPS, weights=E(var2_without_CAPS)$weight, type="barrat")

38 Descriptive Statistics for Barrat Weighted Transitivity by Vertex

summary(var2_without_CAPS_transitivity_barrat[which(var2_without_CAPS_transitivity_barrat != Inf)])

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.3333  0.5345  0.6097  1.0000  2.0000

sd(var2_without_CAPS_transitivity_barrat[which(var2_without_CAPS_transitivity_barrat != Inf)])

## [1] 0.3607665

39 Transitivity Measures Dinamic Table

#Getting  Measures

var2_without_CAPS_transitivity_local<-transitivity(var2_without_CAPS, type="local") %>% round(3)

var2_without_CAPS_transitivity_barrat<-transitivity(var2_without_CAPS, weights=E(var2_without_CAPS)$weight, type="barrat") %>% round(3)

#Creating a datagrame of measures
var2_without_CAPS_transitivity_df <- data.frame(var2_without_CAPS_transitivity_local,var2_without_CAPS_transitivity_barrat) %>% round(3)

40 Transitivity Measures Dinamic Table

var2_without_CAPS_transitivity_df <-cbind(var2_without_CAPS_transitivity_df, V(var2_without_CAPS)$LABEL_COR)

#Adding names
names(var2_without_CAPS_transitivity_df) <- c("Local", "Barrat's Weighted","Type")

#Ordering Variables
var2_without_CAPS_transitivity_df<-var2_without_CAPS_transitivity_df[c("Type", "Local", "Barrat's Weighted")]

40.1 General tabel - DT

datatable(var2_without_CAPS_transitivity_df, filter = 'top')

40.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_transitivity_df, by=list(var2_without_CAPS_transitivity_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Local(M)", "Barrat's Weighted(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

40.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_transitivity_df, function(x) c(median=median(x))) 

names(aggdata_median) <- c("Group","Local(median)", "Barrat's Weighted(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

40.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Local(M)","Local(median)", "Barrat's Weighted(M)","Barrat's Weighted(median)")]

40.5 Final table with round - Transitivity

datatable(total_table, filter = 'top')

41 Transitivity Measures Dinamic Table

#Getting  Measures

var2_without_CAPS_transitivity_local<-transitivity(var2_without_CAPS, type="local") %>% round(3)

var2_without_CAPS_transitivity_barrat<-transitivity(var2_without_CAPS, weights=E(var2_without_CAPS)$weight, type="barrat") %>% round(3)

#Creating a datagrame of measures
var2_without_CAPS_transitivity_df <- data.frame(var2_without_CAPS_transitivity_local,var2_without_CAPS_transitivity_barrat) %>% round(3)

42 Transitivity Measures Dinamic Table

var2_without_CAPS_transitivity_df <-cbind(var2_without_CAPS_transitivity_df, V(var2_without_CAPS)$TIPO1)

#Adding names
names(var2_without_CAPS_transitivity_df) <- c("Local", "Barrat's Weighted","Type")

#Ordering Variables
var2_without_CAPS_transitivity_df<-var2_without_CAPS_transitivity_df[c("Type", "Local", "Barrat's Weighted")]

42.1 General tabel - DT

datatable(var2_without_CAPS_transitivity_df, filter = 'top')

42.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_transitivity_df, by=list(var2_without_CAPS_transitivity_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Local(M)", "Barrat's Weighted(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

42.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_transitivity_df, function(x) c(median=median(x))) 

names(aggdata_median) <- c("Group","Local(median)", "Barrat's Weighted(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

42.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Local(M)","Local(median)", "Barrat's Weighted(M)","Barrat's Weighted(median)")]

42.5 Final table with round - Transitivity

datatable(total_table, filter = 'top')

43 Transitivity Measures Dinamic Table

#Getting  Measures

var2_without_CAPS_transitivity_local<-transitivity(var2_without_CAPS, type="local") %>% round(3)

var2_without_CAPS_transitivity_barrat<-transitivity(var2_without_CAPS, weights=E(var2_without_CAPS)$weight, type="barrat") %>% round(3)

#Creating a datagrame of measures
var2_without_CAPS_transitivity_df <- data.frame(var2_without_CAPS_transitivity_local,var2_without_CAPS_transitivity_barrat) %>% round(3)

44 Transitivity Measures Dinamic Table

var2_without_CAPS_transitivity_df <-cbind(var2_without_CAPS_transitivity_df, V(var2_without_CAPS)$TIPO2)

#Adding names
names(var2_without_CAPS_transitivity_df) <- c("Local", "Barrat's Weighted","Type")

#Ordering Variables
var2_without_CAPS_transitivity_df<-var2_without_CAPS_transitivity_df[c("Type", "Local", "Barrat's Weighted")]

44.1 General tabel - DT

datatable(var2_without_CAPS_transitivity_df, filter = 'top')

44.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_transitivity_df, by=list(var2_without_CAPS_transitivity_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Local(M)", "Barrat's Weighted(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

44.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_transitivity_df, function(x) c(median=median(x))) 

names(aggdata_median) <- c("Group","Local(median)", "Barrat's Weighted(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

44.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[c("Group","Local(M)","Local(median)", "Barrat's Weighted(M)","Barrat's Weighted(median)")]

44.5 Final table with round - Transitivity

datatable(total_table, filter = 'top')

45 Distances and paths

Defined as the shortest distance between each pair of nodes in the network (in both directions for directed graphs).

45.1 Average path length between any two given nodes

Calculates the average path length in a graph, by calculating the shortest paths between all pairs of vertices (both ways for directed graphs).

This function does not consider edge weights currently and uses a breadth-first search.

mean_distance(var2_without_CAPS, directed=T, unconnected = T)

## [1] 3.582102

45.2 Shortest Paths

#Shortest Paths
var2_without_CAPS_sp_in <- shortest.paths(var2_without_CAPS, mode='in', weights=E(var2_without_CAPS)$var2) #in

var2_without_CAPS_sp_out <- shortest.paths(var2_without_CAPS, mode='out', weights=E(var2_without_CAPS)$var2) # out

var2_without_CAPS_sp_all <- shortest.paths(var2_without_CAPS, mode='all', weights=E(var2_without_CAPS)$var2) # all

45.3 Descriptive Shortest Paths - IN

summary(var2_without_CAPS_sp_in[which(var2_without_CAPS_sp_in != Inf)])

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   3.000   3.541   4.000  10.000

sd(var2_without_CAPS_sp_in[which(var2_without_CAPS_sp_in != Inf)])

## [1] 1.809943

45.4 Descriptive Shortest Paths - OUT

summary(var2_without_CAPS_sp_out[which(var2_without_CAPS_sp_out != Inf)])

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   3.000   3.541   4.000  10.000

sd(var2_without_CAPS_sp_out[which(var2_without_CAPS_sp_out != Inf)])

## [1] 1.809943

45.5 Descriptive Shortest Paths - ALL

summary(var2_without_CAPS_sp_all[which(var2_without_CAPS_sp_all != Inf)])

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.000   2.000   2.716   4.000   6.000

sd(var2_without_CAPS_sp_all[which(var2_without_CAPS_sp_all != Inf)])

## [1] 0.9588262

46 Length of all shortest paths in the graph:

#All shortest paths 
distances_dist_all_var2_without_CAPS<-distances(var2_without_CAPS, mode="all", weights=E(var2_without_CAPS)$var2)
#distances_sp_all_var2_without_CAPS

distances_dist_all_var2_without_CAPS[distances_dist_all_var2_without_CAPS=="Inf"]<-NA

#Mean Reachbility by Vertex
distances_sp_all_var2_without_CAPS_vec <- vector()
for (i in 1:vcount(var2_without_CAPS)) {
    distances_sp_all_var2_without_CAPS_vec[i] <- 
    mean(distances_dist_all_var2_without_CAPS[i,],na.rm=T)
}
#Adding to igraph object
V(var2_without_CAPS)$var2_sp_all<-distances_sp_all_var2_without_CAPS_vec

47 In shortest paths

distances_dist_in_var2_without_CAPS<-distances(var2_without_CAPS, mode="in",weights=E(var2_without_CAPS)$var2)
#distances_sp_in_var2_without_CAPS

distances_dist_in_var2_without_CAPS[distances_dist_in_var2_without_CAPS=="Inf"]<-NA

#Mean Reachbility by Vertex
distances_sp_in_var2_without_CAPS_vec <- vector()
for (i in 1:vcount(var2_without_CAPS)) {
    distances_sp_in_var2_without_CAPS_vec[i] <- mean(distances_dist_in_var2_without_CAPS[i,], na.rm=T)
}

#Adding to igraph object
V(var2_without_CAPS)$var2_sp_in<-distances_sp_in_var2_without_CAPS_vec

48 Out shortest paths

distances_dist_out_var2_without_CAPS<-distances(var2_without_CAPS, mode="out", weights=E(var2_without_CAPS)$var2)

distances_dist_out_var2_without_CAPS[distances_dist_out_var2_without_CAPS=="Inf"]<-NA

#Mean Reachbility by Vertex
distances_sp_out_var2_without_CAPS_vec <- vector()
for (i in 1:vcount(var2_without_CAPS)) {
    distances_sp_out_var2_without_CAPS_vec[i] <- 
    mean(distances_dist_out_var2_without_CAPS[i,], na.rm = T)
}

#Adding to igraph object
V(var2_without_CAPS)$var2_sp_out<-distances_sp_out_var2_without_CAPS_vec

49 Reachbility Measures Dinamic Table

#Creating a datagrame of measures
var2_without_CAPS_shortpath_df <- data.frame(distances_sp_in_var2_without_CAPS_vec, distances_sp_out_var2_without_CAPS_vec, distances_sp_all_var2_without_CAPS_vec) %>% round(3)

#Adding type
var2_without_CAPS_shortpath_df <-cbind(var2_without_CAPS_shortpath_df, V(var2_without_CAPS)$LABEL_COR)

#Adding names
names(var2_without_CAPS_shortpath_df) <- c("Short Path IN", "Short Path OUT","Short Path ALL","Type") 

#Ordering Variables
var2_without_CAPS_shortpath_df<-var2_without_CAPS_shortpath_df[c("Type", "Short Path IN", "Short Path OUT","Short Path ALL")]

49.1 General tabel - DT

datatable(var2_without_CAPS_shortpath_df, filter = 'top')

49.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_shortpath_df, by=list(var2_without_CAPS_shortpath_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Short Path IN(M)", "Short Path OUT(M)","Short Path ALL(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

49.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_shortpath_df, function(x) c(median=median(x)))

names(aggdata_median) <- c("Group", "Short Path IN(median)", "Short Path OUT(median)","Short Path ALL(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

49.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[,c("Group","Short Path IN(M)","Short Path IN(median)","Short Path OUT(M)","Short Path OUT(median)","Short Path ALL(M)","Short Path ALL(median)")]

49.5 Final table with round - Short Path

datatable(total_table, filter = 'top')

50 Reachbility Measures Dinamic Table

#Creating a datagrame of measures
var2_without_CAPS_shortpath_df <- data.frame(distances_sp_in_var2_without_CAPS_vec, distances_sp_out_var2_without_CAPS_vec, distances_sp_all_var2_without_CAPS_vec) %>% round(3)

#Adding type
var2_without_CAPS_shortpath_df <-cbind(var2_without_CAPS_shortpath_df, V(var2_without_CAPS)$TIPO1)

#Adding names
names(var2_without_CAPS_shortpath_df) <- c("Short Path IN", "Short Path OUT","Short Path ALL","Type") 

#Ordering Variables
var2_without_CAPS_shortpath_df<-var2_without_CAPS_shortpath_df[c("Type", "Short Path IN", "Short Path OUT","Short Path ALL")]

50.1 General tabel - DT

datatable(var2_without_CAPS_shortpath_df, filter = 'top')

50.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_shortpath_df, by=list(var2_without_CAPS_shortpath_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Short Path IN(M)", "Short Path OUT(M)","Short Path ALL(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

50.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_shortpath_df, function(x) c(median=median(x)))

names(aggdata_median) <- c("Group", "Short Path IN(median)", "Short Path OUT(median)","Short Path ALL(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

50.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[,c("Group","Short Path IN(M)","Short Path IN(median)","Short Path OUT(M)","Short Path OUT(median)","Short Path ALL(M)","Short Path ALL(median)")]

50.5 Final table with round - Short Path

datatable(total_table, filter = 'top')

51 Reachbility Measures Dinamic Table

#Creating a datagrame of measures
var2_without_CAPS_shortpath_df <- data.frame(distances_sp_in_var2_without_CAPS_vec, distances_sp_out_var2_without_CAPS_vec, distances_sp_all_var2_without_CAPS_vec) %>% round(3)

#Adding type
var2_without_CAPS_shortpath_df <-cbind(var2_without_CAPS_shortpath_df, V(var2_without_CAPS)$TIPO2)

#Adding names
names(var2_without_CAPS_shortpath_df) <- c("Short Path IN", "Short Path OUT","Short Path ALL","Type") 

#Ordering Variables
var2_without_CAPS_shortpath_df<-var2_without_CAPS_shortpath_df[c("Type", "Short Path IN", "Short Path OUT","Short Path ALL")]

51.1 General tabel - DT

datatable(var2_without_CAPS_shortpath_df, filter = 'top')

51.2 Aggregating data from previous table - mean

aggdata_mean <-aggregate(var2_without_CAPS_shortpath_df, by=list(var2_without_CAPS_shortpath_df$Type), FUN=mean, na.rm=TRUE)

names(aggdata_mean) <- c("Group","Type","Short Path IN(M)", "Short Path OUT(M)","Short Path ALL(M)")
  
#Removing Type variable
aggdata_mean<-aggdata_mean[,-c(2)]

51.3 Aggregating data from previous table - median

aggdata_median <-aggregate(. ~ Type, var2_without_CAPS_shortpath_df, function(x) c(median=median(x)))

names(aggdata_median) <- c("Group", "Short Path IN(median)", "Short Path OUT(median)","Short Path ALL(median)")

#Removing Type variable
#aggdata_median<-aggdata_median[,-c(2)]

51.4 Merging mean and median

total_table <- merge(aggdata_mean,aggdata_median,by="Group")

#Rounding
Group<-total_table[,c(1)] #Keeping group
total_table<-total_table[,-c(1)] %>% round(3) #Rouding
total_table<-cbind(Group,total_table) #Binding toghter

#Organizing Variabels
total_table<-total_table[,c("Group","Short Path IN(M)","Short Path IN(median)","Short Path OUT(M)","Short Path OUT(median)","Short Path ALL(M)","Short Path ALL(median)")]

51.5 Final table with round - Short Path

datatable(total_table, filter = 'top')

51.6 Histogram from shortest path length between each pair of vertices.

sp<-distance_table(var2_without_CAPS, directed = TRUE)
short_paths<-c(sp$unconnected, sp$res)
labels<-c("unconnected", "one", "two","three", "four", "five", "six")
sphist<-as.data.frame(cbind(labels, short_paths))
names(sphist)<-c("Short Paths Length - Vertex Pairs","Count")
datatable(sphist)

51.7 Simplify Graph - removing loops and duble edges

#var2_without_CAPS_u<-simplify(var2_without_CAPS) #Simplify

var2_without_CAPS_u<-as.undirected(var2_without_CAPS, mode="collapse",edge.attr.comb=list(weight="mean","ignore"))

52 Find cliques (complete subgraphs of an undirected graph)

Graph clique is a subset of vertices of a graph such that every two vertices in the clique are adjacent. - To check*

52.1 Number of cliques - subgraphs

cliques_var2_without_CAPS_u<-cliques(var2_without_CAPS_u) # list of cliques 
length(cliques_var2_without_CAPS_u)

## [1] 3423

52.2 Number of cliques by cliques size

cliques_var2_without_CAPS_u_size<-sapply(cliques(var2_without_CAPS_u), length) 
cliques_var2_without_CAPS_u_size_t<-table(cliques_var2_without_CAPS_u_size)
cliques_var2_without_CAPS_u_size_t

## cliques_var2_without_CAPS_u_size
##   1   2   3   4   5   6   7   8 
## 186 689 930 835 523 208  47   5

52.3 Cliques Bar Plot Sizes Frequency

barplot(cliques_var2_without_CAPS_u_size_t)
title(main = "Cliques Sizes Frequency - Bar Plot 4_REFERENCIA DE RECEBIMENTO CONTRAREFERENCIA (var2)", font.main = 4)

52.4 Size of largest clique

A maximum clique is a clique that cannot be extended by including one more adjacent vertex (not included in larger one).

clique_num(var2_without_CAPS_u)

## [1] 8

52.5 Number of maximal cliques

count_max_cliques(var2_without_CAPS_u)

## [1] 369

52.6 Finding of largest cliques

largest_cliques<-largest_cliques(var2_without_CAPS_u) # cliques with max number of nodes
length(largest_cliques)

## [1] 5

52.7 Plotting the largest cliques - important to consider connectivite

#Coloring largest clique as gold and others one as gray
vcol <- rep("grey80", vcount(var2_without_CAPS_u))
vcol[unlist(largest_cliques(var2_without_CAPS_u))] <- "gold"

#Saving gray and gold as igraph attribute
V(var2_without_CAPS_u)$vcol<-vcol

#Saving labels to display as legend
V(var2_without_CAPS_u)$vcollabel[V(var2_without_CAPS_u)$vcol=="gold"]<-"Largets Clique"
V(var2_without_CAPS_u)$vcollabel [V(var2_without_CAPS_u)$vcol=="grey80"]<-"Others"

52.8 Plotting Clique Size

set.seed(123)
#Plotting based only on degree measures 
edge.start <- ends(var2_without_CAPS_u, es=E(var2_without_CAPS_u), names=F)[,1]

# Fixing ego
minC <- rep(-Inf, vcount(var2_without_CAPS_u))
maxC <- rep(Inf, vcount(var2_without_CAPS_u))
minC[1] <- maxC[1] <- 0
co <- layout_with_fr(var2_without_CAPS_u, niter=10^4, minx=minC, maxx=maxC,miny=minC, maxy=maxC, weights=E(var2_without_CAPS_u)$var2_without_CAPS)

#Plotting
plot(var2_without_CAPS_u, 
     layout=co,
     edge.color=V(var2_without_CAPS_u)$vcol[edge.start],
     #edge.arrow.size=E(var2_without_CAPS_u)$var2_without_CAPS/2000*mean(E(var2_without_CAPS_u)$var2_without_CAPS),
     #edge.width=E(var2_without_CAPS_u)$var2_without_CAPS/20*mean(E(var2_without_CAPS_u)$var2_without_CAPS),
     edge.curved = TRUE,
     vertex.color=vcol,
     vertex.size=log(degree(var2_without_CAPS_u)+2)*10,
     vertex.frame.color="black",
     vertex.label.color="black",
     vertex.label=get.vertex.attribute(var2_without_CAPS_u,"LABEL_COR"),
     vertex.label.cex=log(degree(var2_without_CAPS_u)+2)/10,
     vertex.label.dist=0,
     rescale=F,
     xlim=range(co[,1]), 
     ylim=range(co[,2])
     )
axis(1)
axis(2)

#Solving Problems with legend rendering 
a<-V(var2_without_CAPS_u)$vcollabel
b<-V(var2_without_CAPS_u)$vcol
c<-table(a,b)
d<-as.data.frame(c)
e<-subset(d, d$Freq>0)
f<-t(e$a)
g<-t(e$b)

#Adding Legend
legend(x=range(co[,1])[2], 
       y=range(co[,2])[2],
       legend=as.character(f),
       pch=21,
       col = "#777777", 
       pt.bg=as.character(g),
       pt.cex=2,
       bty="n", 
       ncol=1,
       lty=1,
       cex = .3)


#Adding Title
  title("Network Vertex Degree Sized - classfied by largest clique vs. others", sub = "Source: from authors ")  
  text( 
    x=range(co[,1])[1],
    y=range(co[,2])[1], 
      labels =       sprintf("Size of largest clique: %.1f\nNumber of maximal cliques: %.1f",
     clique_num(var2_without_CAPS_u), 
     count_max_cliques(var2_without_CAPS_u)
             )
       )

# Re-generate dataframes for both nodes and edges, now containing
# calculated network attributes
var2_without_CAPS_node_list <- get.data.frame(var2_without_CAPS, what = "vertices")

#Write Node List
write.csv(var2_without_CAPS_node_list, "~/SNArRDJF/Tese_Pedro/SemCAPS/Banco/var2_without_CAPS_node_list_df.csv")

# Determine a community for each edge. If two nodes belong to the
# same community, label the edge with that community. If not,
# the edge community value is 'NA'
var2_without_CAPS_edge_list <- get.data.frame(var2_without_CAPS, what = "edges")

#Write Node List
write.csv(var2_without_CAPS_edge_list, "~/SNArRDJF/Tese_Pedro/SemCAPS/Banco/var2_without_CAPS_edge_list.csv")

#Write Node List
write.csv(var2_without_CAPS_edge_list, "~/SNArRDJF/Tese_Pedro/SemCAPS/Banco/var2_without_CAPS_edge_list.csv")

53 Saving objects with new variables and changes

save.image("~/SNArRDJF/Robject/var2_without_CAPS_dataframe.RData")